The ultrastructure of the nictitating membrane in the little penguin Eudyptula minor was studied using both scanning and transmission electron microscopy to improve our understanding of the function of ocular adnexa in diving birds. Following euthanasia, eyes were enucleated and immersion fixed in Karnovsky’s fixative. The nictitating membrane and conjunctiva were embedded in araldite and semi- or ultra-thin sections were stained and photographed using compound and transmission electron microscopes, respectively. Ultrastructural dimensions were measured directly from digital photographs. Surface ultrastructure was examined using scanning electron microscopy. The transparent nictitating membrane consists of a dense stroma surrounded by epithelia on both the external (conjunctival) and internal (bulbar) surfaces. The conjunctival surface of the membrane near the leading edge is covered by microvilli, which transition to microplicae and finally to microridges in the periphery. Beneath the epithelial cells, there is a well-developed basement membrane. Scattered throughout this epithelium are a few goblet cells. The surface of the bulbar epithelium is covered by microvilli near the leading edge, which become denser peripherally. The stroma consists of densely-packed collagen fibrils, which are randomly oriented in bundles near the leading edge but are aligned in the same direction parallel with the epithelial and corneal surfaces and with the leading edge, when the membrane is extended. The ultrastructure of the nictitating membrane in the little penguin differs from other birds and its function is predominantly protective, while preserving clear vision in both water and air.